Dear Qing,
I have a couple of more questions to ask you, if you have time. First one
is the blank lines in the resp input file. I have followed the same
procedure for adenosine and DMP. I have created the .dat file and the 1st
and 2nd resp.in files. But I did not understand the blank lines. In your
sample file, u dont use the 7th area, so u have a blank line there. Let me
copy/past those parts:
----------------
.
.
1 0
1 0
6 0.000
1 6 1 14 2 2 2 3 2 4 2 5
6 0.000
1 1 1 9 2 10 2 11 2 12 2 13
--------------
Then, u have described the intermolecular charge constraints. After that
you have 4 blank lines. This is for the 1st resp fit. Why do you have 4
blank lines but not just 1? On the second fit, you have 7 blank lines
after the 6th area (no inter/intramolecular charge constraints and
multiple molecule atom equivalencing is used). How should someone decide
how many blank lines to use?
My 2nd question is about the perl scripts u provide in your sample. My
question is about the 'p_d_q2q.pl' file. The program needs some files in
order to convert the resp output files to an AMBER file. Here is the
command line for this script:
# -----------------------------------------
# To run, type: perl p_d_q2q.pl -p abc.pdb [-p2 abc2.pdb] -q abc.pch -d
# abc.in -o charges.dat
# -- abc.pdb: abc's PDB file
# -- abc2.pdb: second PDB file, if abc.pdb and abc2.pdb produce abc.pch
# together AND
# abc2.pdb produces the 2nd part of abc.pch
# -- abc.pch: charges output file from RESP
# -- abc.in: abc's AMBER database file
# -- charges.dat: charges in the order and format of database file
#
# Qing Zhang, Dept. of Chemistry, New York University
# May. 16, 2002 (freeware, no warranty)
#
# -----------------------------
If we use 2 files (as it is done in the sample) we have to provide both of
these .pdb files in the command line as -p and -p2. -q is just the .pch
output of the resp procedure. I did not understand what is meant by -d and
-o and how to get those files. Thanks in advance for your time.
Best,
On Thu, 7 Jul 2005, Qing Zhang wrote:
> > --- Ilyas Yildirim <yildirim.pas.rochester.edu>
> wrote:
> >
> > Dear Qing Zhang,
> >
> > Thank you very much for your answers. It answered
> > all of the questions I
> > needed to know.:) The only thing that still bugs my
> > mind is the 8th and
> > 9th parts of the resp program (or maybe I am
> > confused a little bit). Is
> > the 7th part the charge constraints when the atoms
> > are within the
> > molecule? For instace, when nmol=1, there can be
> > charge constraints in
> > the molecule. When nmol=2 (or more), the constraints
> > can be between 2-3
> > molecules (which means intermolecular).
>
> You're right.
>
>
> > So, I would
> > guess that in your
> > sample the constraints are intermolecular (which
> > means the 8th and 9th
> > areas are used).
>
> I just looked at the RESP manual and the sample. There
> is one blank line after the 6th area in the sample,
> which means the 7th area (intramolecular charge
> constrain) is not used but the 8th area
> (intermolecular charge constraints) is used. The both
> have the format of
>
> ngrp (I5), grpchg (F10.5)
> imol, iatom (16I5)
>
> The above two lines are for one constraint. In the
> sample, there are two constraints (for DX), which
> occupy 4 lines.
>
> The 9th area is not used in the sample because we do
> not use multiple molecule atom equivalencing, which is
> used to equivalence some backbone atoms between A, T,
> G, C in the force field development. This area has a
> format of
>
> ngrp (I5)
> imol, iatom (16I5)
>
> For more examples, you can look into the RESP sample
> directory in AMBER (at least in version 6 and 7):
> examples/resp_charge_fit/
>
>
> Sincerely,
>
> Qing
>
> ======================================
> Qing Zhang, Ph.D.
> Research Associate
> Molecular Graphics Laboratory
> Department of Molecular Biology, MB-5
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000
> Tel: (858) 784-2202
> Fax: (858) 784-2860
> Email: qzhang.scripps.edu
> ======================================
>
>
>
> ____________________________________________________
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>
--
Ilyas Yildirim
---------------------------------------------------------------
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, # B10 - -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Tue Jul 12 2005 - 02:53:01 PDT
